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1. add variant cray-static, older crays build hpcprof-mpi static,
newer ones build dynamic.
2. move URL patches from github to gitlab.
3. add workaround for a bug where a file is mistakenly overwritten.
4. add conflict for hpcprof-mpi at 2022.10.01.
* [@spackbot] updating style on behalf of mwkrentel
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
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* VTK: add missing dependencies
* Deal with missing verdict dep
* http -> https
* Add patch to fix failing cmake
* Update netcdf-cxx usage in build recipe
* netcdf-cxx4 doesn't work
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* license bump year
* fix black issues of modified files
* mypy
* fix 2021 -> 2023
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* npm: Add latest version, update build
The `npm` package had gotten a bit long in the tooth and only suported the last version
for which running `configure` / `make` / `make install` actually worked.
- [x] Update the package to support npm@9, in which `npm install .` works properly and
installation is easier.
- [x] Update the package so that `npm@6:8` also install successfullly. The incantation
that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node
bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install`
or `npm pack` will fail when run straight from the install directory. So now we just
manually copies things over.
This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least
for me).
udpates the `npm` build to support versions 6-9 and fixes the install for all of
them on macos.
* update for review
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* [armpl-gcc] Make pkg-config files available
ARMpl pkgconfig files are located in a non-default location and do not have the
.pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
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* py-itk: add version 5.3.0
* Remove wheels for unsupported python versions
* Fill out the version specs
* Drop th 'm' from the cp37 version strings
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-Wno-error=incompatible-function-pointer-types,pointer-types-discards-qualifiers (#34984)
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* py-sphinx-immaterial: new package
This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on
the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear
and readable. We *might* consider switching to it for Spack's docs.
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add note about node.js requirements
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* Forward lookup of "test_log_file" and "test_failures"
refers #34531
closes #34487
fixes #34440
* Add unit test
* py-libensemble: fix tests
* Support stand-alone tests with cached files as install-time tests
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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* gnupg: 2.4.0
* libksba: 1.6.3 (CVE-2022-47629)
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This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs.
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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* Add new file for MVAPICH 3.0a release
Creating this as a new package since it requires some new configuration
options and because we are moving to the name "MVAPICH" and droping the
2 (following a similar move by MPICH).
Co-authored-by: Nat Shineman <shineman.5@osu.edu>
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
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Co-authored-by: openCARP consortium <info@opencarp.org>
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Update crtm from JCSDA-EMC spack fork, add crtm-fix
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* OpenCV: checksum for 4.5.5, make contrib optional
* [@spackbot] updating style on behalf of iarspider
* Add conflicts for contrib modules
* Fix typo
* Implement changes from review
* Update var/spack/repos/builtin/packages/opencv/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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There are some declarations that need to be declared noexcept for
valarray. This affects gcc 9.5:11.2.
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* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)"
This reverts commit 891a63cae616dbc92acdad0e0eb626edbd0862a0.
* fix to py-python-multipart, as per PR review
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* py-macs2: add version 2.2.7.1 and support python@3.10:
The tarball from PyPi includes the Cythonized C files. The tarball from
github does not. Remove the Cythonized C files from the source so that
they are rebuilt with the Spack Python/Cython combination. This is
necessary for python-3.10 but make sense for other combinations as well.
* Edits based on review
- set python version constraint on version 2.2.4
- removed all python-2 versions and related constraints.
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* py-xxhash: fix xxhash dependency
The dependency should be xxhash@0.8.0:.
* Add version 3.2.0
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Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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* Add depends_on("mpi") to fix missing <mpi.h>
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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- add python dependency
- add perl dependency
- set python and perl interpreters in scripts
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- stringtie uses internal samtools so remove dependency on samtools
- add dependency for zlib
- use make release target to get correct flags
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* Add package file for xtb and py-xtb
* Retain maintainers from PythonPackage
* Update package files
- use extends("python") instead of tampering with PYTHONPATH
- use PyPI for downloading sdist of py-xtb
- add simple-dftd3 0.7.0
- add dftd4 3.5.0
- remove --wrap-mode=nodownload from toml-f
* Remove logic for download URL
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This reverts commit 4e63d92bc927aeb5380bdc48500abda4cda4b5bd.
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Packages that use docbook-xml may specify a specific entity version.
When this is specified as a version constraint in the package recipe it
will cause problems when using `unify = True` in a Spack environment, as
there could be multiple versions of docbook-xml in the spec. In
practice, any entity version should work with any other version and
everything should work with the latest version. This PR maps all Spack
docbook-xml entity versions to the docbook-xml version in the spec.
Ideally, the version in the spec would be the latest version. With this
PR, even if a package specifies an older entity version, it will map
to the entity version (latest) in the spec. This means that there can be one
docbook-xml version in a Spack environment spec and packages requesting
older entity versions will still work.
To help facilitate this, docbook-xml version constraints for packages
that have them have been removed. Those packages are dbus and gtk-doc.
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A few new versions of harbuzz, but just jumping to the last non-6 version as preferred.
No build system changes:
- within 5 series: https://github.com/harfbuzz/harfbuzz/compare/5.1.0...5.3.1
- from 5 to 6: https://github.com/harfbuzz/harfbuzz/compare/5.3.1...6.0.0
The 5 series fixes a build issue for aarch64, https://github.com/harfbuzz/harfbuzz/issues/3768.
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